Oakland Athletics manager Bob Melvin, right, speaks to home plate umpire Chad Fairchild in the second inning of a baseball game against the Toronto Blue Jays Thursday, July 3, 2014, in Oakland, Calif. The A's are playing the game under protest. (AP Photo/Ben Margot)

Photo: Ben Margot, Associated Press

Oakland Athletics manager Bob Melvin, right, speaks to home plate...

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OAKLAND, CA - JULY 03: Brandon Moss #37 of the Oakland Athletics slides into second base with a double, beating the tag of Munenori Kawasaki #66 of the Toronto Blue Jays in the bottom of the six inning at O.co Coliseum on July 3, 2014 in Oakland, California. (Photo by Thearon W. Henderson/Getty Images)

OAKLAND, CA - JULY 03: Alberto Callaspo #7 of the Oakland Athletics hits a sacrifice fly, scoring John Jaso (not pictured) in the bottom of the eighth inning against the Toronto Blue Jays at O.co Coliseum on July 3, 2014 in Oakland, California. (Photo by Thearon W. Henderson/Getty Images)

Photo: Thearon W. Henderson, Getty Images

OAKLAND, CA - JULY 03: Alberto Callaspo #7 of the Oakland...

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OAKLAND, CA - JULY 03: Craig Gentry #3 of the Oakland Athletics slides into home safe ahead of the throw to catcher Josh Thole #22 of the Toronto Blue Jay in the bottom of the eighth inning at O.co Coliseum on July 3, 2014 in Oakland, California. Gentry scored on an RBI double from John Jaso. (Photo by Thearon W. Henderson/Getty Images)

Photo: Thearon W. Henderson, Getty Images

OAKLAND, CA - JULY 03: Craig Gentry #3 of the Oakland Athletics...

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OAKLAND, CA - JULY 03: Craig Gentry #3 of the Oakland Athletics rounds third base to score on an RBI double by John Jaso (not pictured) in the bottom of the eighth inning against the Toronto Blue Jays at O.co Coliseum on July 3, 2014 in Oakland, California. (Photo by Thearon W. Henderson/Getty Images)

Photo: Thearon W. Henderson, Getty Images

OAKLAND, CA - JULY 03: Craig Gentry #3 of the Oakland Athletics...

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OAKLAND, CA - JULY 03: John Jaso #5 of the Oakland Athletics is congratulated by Brandon Moss #37 after Jaso scored in the bottom of the eighth inning against the Toronto Blue Jays at O.co Coliseum on July 3, 2014 in Oakland, California. Jaso scored on a sacrifice fly from Alberto Callaspo #7.. (Photo by Thearon W. Henderson/Getty Images)

Photo: Thearon W. Henderson, Getty Images

OAKLAND, CA - JULY 03: John Jaso #5 of the Oakland Athletics is...

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OAKLAND, CA - JULY 03: Munenori Kawasaki #66 of the Toronto Blue Jays leads off first base against the Oakland Athletics in the top of the fourth inning at O.co Coliseum on July 3, 2014 in Oakland, California. (Photo by Thearon W. Henderson/Getty Images)

Photo: Thearon W. Henderson, Getty Images

OAKLAND, CA - JULY 03: Munenori Kawasaki #66 of the Toronto Blue...

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OAKLAND, CA - JULY 03: Munenori Kawasaki #66 of the Toronto Blue Jays dives back into first base safe beating the throw over to Nate Freiman #35 of the Oakland Athletics in the top of the fourth inning at O.co Coliseum on July 3, 2014 in Oakland, California. (Photo by Thearon W. Henderson/Getty Images)

Photo: Thearon W. Henderson, Getty Images

OAKLAND, CA - JULY 03: Munenori Kawasaki #66 of the Toronto Blue...

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Oakland Athletics' Sean Doolittle, right, celebrates a 4-1 defeat of the Toronto Blue Jays with catcher Stephen Voght at the end of a baseball game on Thursday, July 3, 2014, in Oakland, Calif. (AP Photo/Ben Margot)

Photo: Ben Margot, Associated Press

Oakland Athletics' Sean Doolittle, right, celebrates a 4-1 defeat...

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Seetha Narayanan, of Saratoga, cheers at the Oakland Coliseum during the Oakland Athletics game on Thursday, July 3, 2014 in Oakland, Calif.

Photo: Beck Diefenbach, Special To The Chronicle

Seetha Narayanan, of Saratoga, cheers at the Oakland Coliseum...

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Oakland Athletics' Sean Doolittle works against the Toronto Blue Jays in the ninth inning of a baseball game on Thursday, July 3, 2014, in Oakland, Calif. (AP Photo/Ben Margot)

Photo: Ben Margot, Associated Press

Oakland Athletics' Sean Doolittle works against the Toronto Blue...

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Oakland Athletics' mascot Stomper walks through through the Oakland Coliseum during the Oakland Athletics game on Thursday, July 3, 2014 in Oakland, Calif.

Photo: Beck Diefenbach, Special To The Chronicle

Oakland Athletics' mascot Stomper walks through through the Oakland...

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Mackenzie Ussery, 14, of Turlock, sports he Oakland Athletic's headband during the Oakland Athletics game on Thursday, July 3, 2014 in Oakland, Calif.

Photo: Beck Diefenbach, Special To The Chronicle

Mackenzie Ussery, 14, of Turlock, sports he Oakland Athletic's...

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Zak McCasland (left), 10, and Matthew Jensen, 12, watch the Oakland Athletics play the Toronto Blue Jays at the Oakland Coliseum on Thursday, July 3, 2014 in Oakland, Calif.

Oakland Athletics' Craig Gentry (3) is cogratulated after scoring against the Toronto Blue Jays in the eighth inning of a baseball game on Thursday, July 3, 2014, in Oakland, Calif. Gentry scored on a double hit by John Jaso. (AP Photo/Ben Margot)

Photo: Ben Margot, Associated Press

Oakland Athletics' Craig Gentry (3) is cogratulated after scoring...

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Toronto Blue Jays' second baseman Munenori Kawasaki completes a double play throw over Oakland Athletics' Craig Gentry (3) in the fifth inning of a baseball game Thursday, July 3, 2014, in Oakland, Calif. A's John Jaso was out at first base. (AP Photo/Ben Margot)

Photo: Ben Margot, Associated Press

Toronto Blue Jays' second baseman Munenori Kawasaki completes a...

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Eric Tallista and his nephew River Dixon, 12, both of Benicia, sing "Take Me Out to the Ballgame" at the Oakland Coliseum during the Oakland Athletics game on Thursday, July 3, 2014 in Oakland, Calif.

Photo: Beck Diefenbach, Special To The Chronicle

Eric Tallista and his nephew River Dixon, 12, both of Benicia, sing...

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Exuberant fans in the bleachers section cheer on their team at the Oakland Coliseum during the Oakland Athletics game on Thursday, July 3, 2014 in Oakland, Calif.

Photo: Beck Diefenbach, Special To The Chronicle

Exuberant fans in the bleachers section cheer on their team at the...

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David Connell (left), 16, of San Leandro, and his cousin John Karczewski, 13, of Danville, waits for their aunt to arrive at the ticket gate at the Oakland Coliseum before the Oakland Athletics game on Thursday, July 3, 2014 in Oakland, Calif.

Photo: Beck Diefenbach, Special To The Chronicle

David Connell (left), 16, of San Leandro, and his cousin John...

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OAKLAND, CA - JULY 03: Edwin Encarnacion #10 of the Toronto Blue Jays watches the ball go over his head for a double off the bat of Stephen Vogt (not pictured) of the Oakland Athletics in the bottom of the second inning at O.co Coliseum on July 3, 2014 in Oakland, California. (Photo by Thearon W. Henderson/Getty Images)

Photo: Thearon W. Henderson, Getty Images

OAKLAND, CA - JULY 03: Edwin Encarnacion #10 of the Toronto Blue...

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Zak McCasland 10, takes part in a "wave" during the Oakland Athletics game against the Toronto Blue Jays at the Oakland Coliseum on Thursday, July 3, 2014 in Oakland, Calif.

Photo: Beck Diefenbach, Special To The Chronicle

Zak McCasland 10, takes part in a "wave" during the Oakland...

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Fans traverse sections at the Oakland Coliseum during the Oakland Athletics game against the Toronto Blue Jays on Thursday, July 3, 2014 in Oakland, Calif.

Baseball's replay system remains a work in progress. In the A's 4-1 victory over Toronto on Thursday night, common sense seemingly took a hit when replay was applied.

In the second inning, the Jays had loaded the bases against Sonny Gray with one out. Anthony Gose sent a grounder to first baseman Nate Freiman, who appeared to tag Munenori Kawasaki on his way to second. However, first-base ump Vic Carapazza ruled Kawasaki safe.

Freiman then threw to the plate in plenty of time to cut down Edwin Encarnacion. Catcher Stephen Vogt didn't tag Encarnacion, understandably thinking a force play was in effect.

So, it seemed as if the Jays still would have the bases loaded with two outs in a 0-0 game. Except, enter Toronto manager John Gibbons and his challenge of the call on Freiman's tag.

After a lengthy review, Kawasaki was ruled out, but because Vogt hadn't tagged Encarnacion, the ruling meant Encarnacion had scored and Toronto led 1-0. Again, you can't fault Vogt for not tagging Encarnacion; he was going off Carapazza's safe call.

If there ever was an instance when common sense should prevail over a strict replay interpretation, this would have been it. Probably thinking along those lines, A's manager Bob Melvin played the game under protest.

Per statistician David Feldman, the previous game the A's played under protest came against Seattle exactly 11 years ago Thursday. On July 3, 2003, manager Ken Macha lodged a protest in a game Oakland eventually won 5-2. The Mariners' manager that day? None other than Melvin.

Of course, Thursday's protest became moot when the A's won. As for how the Blue Jays benefited with a run on that play, well, all new systems have their kinks.

"Replay's a new dimension to this game and there are going to be quirks and funny plays like this that happen," crew chief Bill Miller said. "Unfortunately, it happened to us."

In a sense, it really happened to Gray. Not only did the Jays take the lead on the ruling, but Gray endured that lengthy delay while the replay process unfolded. He responded by getting Josh Thole on a grounder to short to end the inning.

"I knew there that the inning had the potential to escalate very quickly," Gray said. "It was very important just to get that guy out and move on."

Coming off a rough outing (five runs on seven hits in five innings) in Miami on Saturday, Gray limited the Jays to a run on four hits in seven innings. He pointed to an improved curveball for his improved results.